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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaacatgtttttattgactcaacatagatccactatataaagtatataaactgttctagccatacatgcaagacaattattttgacaaattttcttttgttgttccaacag

Basic information

species Zea mays
transcript GRMZM2G450055_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G450055_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 5'ss of exon 12
AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaacatgttt-ttattgactcaacatagatccac-tatataaagtatataaactgttctagccatacatgcaagacaattattttgacaaattttcttttgttgttccaacag
 || || ||||||||||||||||||||||||||||||||||||||||| || || || ||||||||||||||||||||||| ||||| ||||||||||||||  || ||  | ||| |||||||||     ||  | ||  | |  ||| | ||| ||| ||||||||| || ||||||| |||| | ||||||| ||||||| ||| |  |||  |||
CATCTCGATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACCTCGGTACTAGCAGCTGCCAATCCAATTGCAGGGCGCTACGATGATCTTAAGgtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagccttatatgcaaggcaatcagtttgacacattttctattgctactcct-cag

upper sequence: GRMZM2G450055_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA17G11220.1 (Glycine max), 5'ss of exon 11
AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaacatgtttttattgactcaacatagatccactatataaagtatataaactgttctagccat-acatgcaa--gacaattattttgacaaattttcttttgttgttccaacag
 |||||||| |||||||| || || ||||| || || ||||||||||||||||||||||| |||||||| ||     |||| || || ||||||||||||||     | |||   | | ||   | | | |   |   || |||  |    | |||   |  ||| ||| ||| |  |  || |  |   ||||    |||||                 
TATATCTATAGCCAAAGCAGGAATAACAACTGTTCTTAATTCAAGGACTTCAGTTCTTGCTGCTGCCAACCCTCCATCAGGCCGATACGATGATCTTAAGgtctactatcataactctctt---ttatctt---ttttctgtatgta----acaaagcataatagtcattacaagagactgatagctgccttgaatgtttttccag--------------

upper sequence: GRMZM2G450055_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA13G22420.1 (Glycine max), 5'ss of exon 11
AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaacatgtttttattgactcaacatagatccactatataaagtatataaactgttctagccatacatgcaagacaattattttgacaaattttcttttgttgttccaacag
 |||||||| ||||||||||| || ||||| || || ||||||||||||||||||||||| |||||||| ||     |||| || || ||||||||||||||     | ||| |     |    |  |  |   | || | | ||||    | |   | |  |    | |   |    | |  |   || |    |||||                 
TATATCTATAGCCAAAGCTGGAATAACAACTGTTCTTAATTCAAGGACTTCAGTTCTTGCTGCTGCCAACCCTCCATCAGGCCGATACGATGATCTTAAGgtctactaccatataaccctc--ttttatcttttttcagtttgtaaa----aaagcatatcgtcattaaaagagactaatagctgcctttaatgtttttccag--------------

upper sequence: GRMZM2G450055_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 5'ss of exon 11
AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaacatgtttttattgactcaacatagatccactatataaagtatataaactgttctagccatacatgcaagacaattattttgacaaattttcttttgttgttccaacag
 ||||| ||||||||||| || || ||||| || || ||||| || ||||| || ||||||||||| || |||    ||||||| |||||||||||||||||   |   |     |||  |  ||||  ||   | |  ||  |    |||  |   || |   |   |||     || ||| || |   || |  |   ||               
CATATCCATTGCCAAAGCGGGAATAACAACTGTGCTTAATTCTAGAACTTCTGTGCTTGCAGCTGCTAACCCACCATCAGGACGTTATGATGATCTTAAGgtccatggcc---ccttttcttcctcag-atttgttctttacttcttatattca---tgcttatgatttactaagcaggcaactaataaaactacatacattccag-----------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211539706|gb|FK958374.1|FK958374
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGGCGCTATGACGATCTTAAG                         ACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
EST: gi|22473461|gb|BU037941.1|BU037941
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGGCGCTATGACGATCTTAAG                         ACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
EST: gi|22490113|gb|BU050036.1|BU050036
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGGCGCTATGACGATCTTAAG                         ACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
EST: gi|22473134|gb|BU037614.1|BU037614
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGGCGCTATGACGATCTTAAG                         ACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
EST: gi|211539705|gb|FK958373.1|FK958373
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAG                         ACTGCACAAGATAATATTGATCTACAGACC
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACC
EST: gi|211542714|gb|FK958381.1|FK958381
EST:     CAGTTCTTGCAGCTGC-AATTCAAATGCAGGACGCTATGATGATCTTAAG                         ACTGCACA-GATAATATTGATCTACAGACCACCAT-CTTTCTAGAATTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
EST: gi|21760083|gb|BQ635624.1|BQ635624
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGGCGCTATGACGATCTTAAG                         ACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
EST: gi|211542715|gb|FK958382.1|FK958382
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGGCGCTATGACGATCTTAAG                         ACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
EST: gi|22545894|gb|BU098253.1|BU098253
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGGCGCTATGACGATCTTAAG                         ACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
EST: gi|211539703|gb|FK958371.1|FK958371
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAG                         ACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGATCAAATCTTTATTGTCAAAGATATCAGAATGTATGACCAAGATAAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 68

AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGATCAAATCTTTATTGTCAAAGATATCAGAATGTATGACCAAGATAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 21

AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGATCAAATCTTTATTGTCAAAGATATCAGAATGTATGACCAAGATAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 23

AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... gttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGATCAAATCTTTATTGTCAAAGATATCAGAATGTATGACCAAGATAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaacatgtttttattgactcaacatagatccactatataaagtatataaactgttctagccatacatgcaagacaattattttgacaaattttcttttgttgttccaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC